Over the past decades, significant progress has been made regarding the quantification and mechanistic understanding of stable carbon isotope fractionation (13C fractionation) in photosynthetic unicellular organisms in response to changes in the partial pressure of atmospheric CO2 (pCO2). However, hardly any data is available for organic cyst-forming dinoflagellates while this is an ecologically important group with a unique fossil record. We performed dilute batch experiments with four harmful dinoflagellate species known for their ability to form organic cysts: Alexandrium tamarense, Scrippsiella trochoidea, Gonyaulax spinifera and Protoceratium reticulatum. Cells were grown at a range of dissolved CO2 concentrations characterizing past, modern and projected future values (∼5–50 μmol L-1), representing atmospheric pCO2 of 180, 380, 800 and 1200 μatm. In all tested species, 13C fractionation depends on CO2 with a slope of up to 0.17‰ (μmol L)-1. Even more consistent correlations were found between 13C fractionation and the combined effects of particulate organic carbon quota (POC quota; pg C cell-1) and CO2. Carbon isotope fractionation as well as its response to CO2 is species-specific. These results may be interpreted as a first step towards a proxy for past pCO2 based on carbon isotope ratios of fossil organic dinoflagellate cysts. However, additional culture experiments focusing on environmental variables other than pCO2, physiological underpinning of the recorded response, testing for possible offsets in 13C values between cells and cysts, as well as field calibration studies are required to establish a reliable proxy.